[R] Fwd: Huge memory utilization when using doMC library

[Srikanth Gumma]

Hi,

I'm the administrator of HPC cluster and one of the user reported that their
R job is vary slow. Below is the code that the user provided to me. May I
request your suggestion why the code is so slow and utilizing 100% memory?

I have installed R version 3.1.2 and RJags_3-14.


## data ##
set.seed(2015)
N <- 1000
y.i <- rnorm(N, 10, 0.1)


## set up MCMC ##
mcmc.chains    <- 3
ChainIDs       <- seq(1, mcmc.chains)
mcmc.burnin    <- 2
N.STEPS        <- 2
n.iter.perstep <- 3
mcmc.thin      <- 1

mort.parameters <- c("mu")
mort.data <- list(y.i = y.i, N = N)

jagsStep.dir <- paste0("JAGSoutput/")
dir.create("JAGSoutput/", showWarnings = FALSE)

library(foreach)
library(R2jags)
library(doMC) ## for linux server only
registerDoMC(4)

## start MCMC

foreach(chain = ChainIDs) %dopar% {

   chain*chain

  set.seed(2013 + chain * 1000)
  rnorm(chain)

  mod <- jags(data = mort.data, #inits = mort.inits,
              parameters.to.save = mort.parameters,
              model.file = "test.txt",
              jags.seed = chain,
              n.chains = 1, n.iter = n.iter.perstep + mcmc.burnin,
              n.burnin = mcmc.burnin, n.thin = mcmc.thin, DIC = TRUE)

}#end of chain loop

## the end ##

Thanks in advance.

Regards
Srikanth.

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